Showing papers on "Hydrogen bond published in 2014"

Erratum: The amyloid state and its association with protein misfolding diseases

Abstract: Nature Reviews Molecular Cell Biology 15, 384–396 (2014) In the legend of figure 2 of the above article (page 388), the sentence “The spacing between polypeptide chains along the fibril axis is constant to a good approximation even for very different polypeptide sequences, a generic property arisingfrom the common inter-side chain hydrogen bonding constraints (orange line in part b).

The hydrophobic effect revisited--studies with supramolecular complexes imply high-energy water as a noncovalent driving force.

Abstract: Traditional descriptions of the hydrophobic effect on the basis of entropic arguments or the calculation of solvent-occupied surfaces must be questioned in view of new results obtained with supramolecular complexes. In these studies, it was possible to separate hydrophobic from dispersive interactions, which are strongest in aqueous systems. Even very hydrophobic alkanes associate significantly only in cavities containing water molecules with an insufficient number of possible hydrogen bonds. The replacement of high-energy water in cavities by guest molecules is the essential enthalpic driving force for complexation, as borne out by data for complexes of cyclodextrins, cyclophanes, and cucurbiturils, for which complexation enthalpies of up to -100 kJ mol(-1) were reached for encapsulated alkyl residues. Water-box simulations were used to characterize the different contributions from high-energy water and enabled the calculation of the association free enthalpies for selected cucurbituril complexes to within a 10% deviation from experimental values. Cavities in artificial receptors are more apt to show the enthalpic effect of high-energy water than those in proteins or nucleic acids, because they bear fewer or no functional groups in the inner cavity to stabilize interior water molecules.

CH–π hydrogen bonds in biological macromolecules

Abstract: This is a sequel to the previous Perspective “The CH–π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates”, which featured in a PCCP themed issue on “Weak Hydrogen Bonds – Strong Effects?”: Phys. Chem. Chem. Phys., 2011, 13, 13873–13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH–π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH–π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH–π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH–π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.

The structure of interfacial water on gold electrodes studied by x-ray absorption spectroscopy

Abstract: The molecular structure of the electrical double layer determines the chemistry in all electrochemical processes. Using x-ray absorption spectroscopy (XAS), we probed the structure of water near gold electrodes and its bias dependence. Electron yield XAS detected at the gold electrode revealed that the interfacial water molecules have a different structure from those in the bulk. First principles calculations revealed that ~50% of the molecules lie flat on the surface with saturated hydrogen bonds and another substantial fraction with broken hydrogen bonds that do not contribute to the XAS spectrum because their core-excited states are delocalized by coupling with the gold substrate. At negative bias, the population of flat-lying molecules with broken hydrogen bonds increases, producing a spectrum similar to that of bulk water.

Contribution of hydrogen bonds to protein stability

Abstract: Our goal was to gain a better understanding of the contribution of the burial of polar groups and their hydrogen bonds to the conformational stability of proteins. We measured the change in stability, Δ(ΔG), for a series of hydrogen bonding mutants in four proteins: villin headpiece subdomain (VHP) containing 36 residues, a surface protein from Borrelia burgdorferi (VlsE) containing 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa (RNase Sa) and T1 (RNase T1). Crystal structures were determined for three of the hydrogen bonding mutants of RNase Sa: S24A, Y51F, and T95A. The structures are very similar to wild type RNase Sa and the hydrogen bonding partners form intermolecular hydrogen bonds to water in all three mutants. We compare our results with previous studies of similar mutants in other proteins and reach the following conclusions. (1) Hydrogen bonds contribute favorably to protein stability. (2) The contribution of hydrogen bonds to protein stability is strongly context dependent. (3) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (4) Polar group burial can make a favorable contribution to protein stability even if the polar groups are not hydrogen bonded. (5) The contribution of hydrogen bonds to protein stability is similar for VHP, a small protein, and VlsE, a large protein.

Crystal Packing of Low-Sensitivity and High-Energy Explosives

Abstract: Low-sensitivity and high-energy explosives (LSHEs) are highly desired for their comprehensive superiority of safety and energy. Crystal packing is crucial to both the safety and energy, and therefore becomes of interest in energetic crystal engineering. This work carries out systemic analyses on the crystal packing of 11 existing LSHEs with both energy and safety close or superior to TNT. As a result, we find that the LSHE crystals wholly feature π–π stacking with the aid of intermolecular hydrogen bonding. Each LSHE molecule is π-bonded with a big conjugated structure composed of all non-hydrogen atoms in the entire molecule. Intramolecular hydrogen bonding exists in most LSHE molecules with strongly active hydrogen bond (HB) donors of amino and hydroxyl groups, and various strength. These big π-conjugated structures and intramolecular HBs lead to planar molecules with high stability, settling a base of π–π stacking in crystals. With the help of intermolecular HBs, the π–π stacking holding the LSHE cryst...

Experimental and Computational Studies of Choline Chloride-Based Deep Eutectic Solvents

Abstract: Choline-chloride based deep eutectic solvents (DES) have been used for several different applications (e.g., solubility, electrochemistry, and purifications) due to their relative inexpensive and readily available nature. In this work, three choline chloride-based DESs are simulated using molecular dynamics to study the hydrogen bonding interactions of the system. Three hydrogen bond donors (HBD) are studied in order to determine the changes in the hydrogen bonding interactions when the HBD is different in the DES. One dicarboxylic acid and two polyols (with different number of OH groups) were chosen as the HBDs of interest. First, the simulations are validated by comparing simulated and experimental thermodynamic and transport properties, when possible. Then, for maline (choline chloride/malonic acid), the more anomalous system studied here, molecular simulations complement results obtained from an FTIR spectroscopic study in order to further understand this unique system. Good agreement with experimenta...

A Robust Binary Supramolecular Organic Framework (SOF) with High CO2 Adsorption and Selectivity

Abstract: A robust binary hydrogen-bonded supramolecular organic framework (SOF-7) has been synthesized by solvothermal reaction of 1,4-bis-(4-(3,5-dicyano-2,6-dipyridyl)dihydropyridyl)benzene (1) and 5,5′-bis-(azanediyl)-oxalyl-diisophthalic acid (2). Single crystal X-ray diffraction analysis shows that SOF-7 comprises 2 and 1,4-bis-(4-(3,5-dicyano-2,6-dipyridyl)pyridyl)benzene (3); the latter formed in situ from the oxidative dehydrogenation of 1. SOF-7 shows a three-dimensional four-fold interpenetrated structure with complementary O–H···N hydrogen bonds to form channels that are decorated with cyano and amide groups. SOF-7 exhibits excellent thermal stability and solvent and moisture durability as well as permanent porosity. The activated desolvated material SOF-7a shows high CO2 adsorption capacity and selectivity compared with other porous organic materials assembled solely through hydrogen bonding.

Recent Advances in the Applications of Ionic Liquids in Protein Stability and Activity: A Review

Abstract: Room temperatures ionic liquids are considered as miraculous solvents for biological system. Due to their inimitable properties and large variety of applications, they have been widely used in enzyme catalysis and protein stability and separation. The related information present in the current review is helpful to the researchers working in the field of biotechnology and biochemistry to design or choose an ionic liquid that can serve as a noble and selective solvent for any particular enzymatic reaction, protein preservation and other protein based applications. We have extensively analyzed the methods used for studying the protein–IL interaction which is useful in providing information about structural and conformational dynamics of protein. This can be helpful to develop and understanding about the effect of ionic liquids on stability and activity of proteins. In addition, the affect of physico-chemical properties of ionic liquids, viz. hydrogen bond capacity and hydrophobicity on protein stability are discussed.

Microscopic insights into the protein-stabilizing effect of trimethylamine N-oxide (TMAO).

Abstract: Although it is widely known that trimethylamine N-oxide (TMAO), an osmolyte used by nature, stabilizes the folded state of proteins, the underlying mechanism of action is not entirely understood. To gain further insight into this important biological phenomenon, we use the C≡N stretching vibration of an unnatural amino acid, p-cyano-phenylalanine, to directly probe how TMAO affects the hydration and conformational dynamics of a model peptide and a small protein. By assessing how the lineshape and spectral diffusion properties of this vibration change with cosolvent conditions, we are able to show that TMAO achieves its protein-stabilizing ability through the combination of (at least) two mechanisms: (i) It decreases the hydrogen bonding ability of water and hence the stability of the unfolded state, and (ii) it acts as a molecular crowder, as suggested by a recent computational study, that can increase the stability of the folded state via the excluded volume effect.

Control of Crystalline Proton-Conducting Pathways by Water-Induced Transformations of Hydrogen-Bonding Networks in a Metal–Organic Framework

Abstract: Structure-defined metal-organic frameworks (MOFs) are of interest because rational design and construction allow us to develop good proton conductors or possibly control the proton conductivity in solids. We prepared a highly proton-conductive MOF (NH4)2(adp)[Zn2(ox)3]·nH2O (abbreviated to 1·nH2O, adp: adipic acid, ox: oxalate, n = 0, 2, 3) having definite crystal structures and showing reversible structural transformations among the anhydrate (1), dihydrate (1·2H2O), and trihydrate (1·3H2O) phases. The crystal structures of all of these phases were determined by X-ray crystallography. Hydrogen-bonding networks consisting of ammonium ions, water molecules, and carboxylic acid groups of the adipic acids were formed inside the two-dimensional interlayer space in hydrated 1·2H2O and 1·3H2O. The crystal system of 1 or 1·2H2O (P21/c, No. 14) was changed into that of 1·3H2O (P1, No. 2), depending on water content because of rearrangement of guests and acidic molecules. Water molecules play a key role in proton conduction as conducting media and serve as triggers to change the proton conductivity through reforming hydrogen-bonding networks by water adsorption/desorption processes. Proton conductivity was consecutively controlled in the range from ∼10(-12) S cm(-1) (1) to ∼10(-2) S cm(-1) (1·3H2O) by the humidity. The relationships among the structures of conducting pathways, adsorption behavior, and proton conductivity were investigated. To the best of our knowledge, this is the first example of the control of a crystalline proton-conducting pathway by guest adsorption/desorption to control proton conductivity using MOFs.

Dissolution Mechanism of Cellulose in N,N-Dimethylacetamide/Lithium Chloride: Revisiting through Molecular Interactions

Abstract: Understanding the interactions between solvent molecules and cellulose at a molecular level is still not fully achieved in cellulose/N,N-dimethylacetamide (DMAc)/LiCl system. In this paper, cellobiose was used as the model compound of cellulose to investigate the interactions in cellulose/DMAc/LiCl solution by using Fourier transform infrared spectroscopy (FTIR), 13C, 35Cl, and 7Li nuclear magnetic resonance (NMR) spectroscopy and conductivity measurements. It was found that when cellulose is dissolved in DMAc/LiCl cosolvent system, the hydroxyl protons of cellulose form strong hydrogen bonds with the Cl–, during which the intermolecular hydrogen bonding networks of cellulose is broken with simultaneous splitting of the Li+–Cl– ion pairs. Simultaneously, the Li+ cations are further solvated by free DMAc molecules, which accompany the hydrogen-bonded Cl– to meet electric balance. Thereafter, the cellulose chains are dispersed in molecular level in the solvent system to form homogeneous solution. This work ...

Probing molecular interaction in ionic liquids by low frequency spectroscopy: Coulomb energy, hydrogen bonding and dispersion forces

Abstract: Ionic liquids are defined as salts composed solely of ions with melting points below 100 °C. These remarkable liquids have unique and fascinating properties and offer new opportunities for science and technology. New combinations of ions provide changing physical properties and thus novel potential applications for this class of liquid materials. To a large extent, the structure and properties of ionic liquids are determined by the intermolecular interaction between anions and cations. In this perspective we show that far infrared and terahertz spectroscopy are suitable methods for studying the cation–anion interaction in these Coulomb fluids. The interpretation of the measured low frequency spectra is supported by density functional theory calculations and molecular dynamics simulations. We present results for selected aprotic and protic ionic liquids and their mixtures with molecular solvents. In particular, we focus on the strength and type of intermolecular interaction and how both parameters are influenced by the character of the ions and their combinations. We show that the total interaction between cations and anions is a result of a subtle balance between Coulomb forces, hydrogen bonds and dispersion forces. For protic ionic liquids we could measure distinct vibrational modes in the low frequency spectra indicating clearly the cation–anion interaction characterized by linear and medium to strong hydrogen bonds. Using isotopic substitution we have been able to dissect frequency shifts related to pure interaction strength between cations and anions and to different reduced masses only. In this context we also show how these different types of interaction may influence the physical properties of ionic liquids such as the melting point, viscosity or enthalpy of vaporization. Furthermore we demonstrate that low frequency spectroscopy can also be used for studying ion speciation. Low vibrational features can be assigned to contact ion pairs and solvent separated ion pairs. In conclusion we showed how detailed knowledge of the low frequency spectra can be used to understand the change in interaction strength and structure by variation of temperature, solvent polarity and solvent concentration in ionic liquids and their mixtures with molecular solvents. In principle the used combination of methods is suitable for studying intermolecular interaction in pure molecular liquids and their solutions including additive materials such as nanoparticles.

Wetting of graphene oxide: a molecular dynamics study.

Abstract: We characterize the wetting properties of graphene oxide by performing classical molecular dynamics simulations. With oxygen-containing functional groups on the basal plane, graphene becomes hydrophilic and the water contact angle decreases with their concentration, c. The concentration dependence displays a transition at c ≈ 11% as defined by the interacting range of hydrogen bonds with oxidized groups and water. Patterns of the oxidized region and the morphological corrugation of the sheet strongly influence the spreading of water droplets with their lateral spans defined by corresponding geometrical parameters and thus can be used to control their behavior on the surface. These results are discussed with respect to relevant applications in graphene oxide-derived functional materials and offer a fundamental understanding of their wetting and flow phenomena.

Self-assembly of hydrogen-bonded two-dimensional quasicrystals

Abstract: Scanning tunnelling microscopy reveals that molecules of ferrocenecarboxylic acid can self-assemble into quasicrystal monolayers containing highly unusual cyclic hydrogen-bonded pentamers; this molecular framework could form the basis of a large range of supramolecular assemblies. The range of systems in which non-periodic quasicrystalline ordering has been observed continues to increase, with small-molecule self-assembled monolayers now entering the arena. Specifically, Natalie Wasio and colleagues find that the hydrogen-bonding patterns of ferrocenecarboxylic acid drive the assembly of these molecules into unusual cyclic pentamers, whose five-fold symmetry facilitates a two-dimensional quasicrystalline arrangement. The authors anticipate that a large range of novel quasicrystalline supramolecular assemblies could be formed based on this molecular framework. The process of molecular self-assembly on solid surfaces is essentially one of crystallization in two dimensions, and the structures that result depend on the interplay between intermolecular forces and the interaction between adsorbates and the underlying substrate1. Because a single hydrogen bond typically has an energy between 15 and 35 kilojoules per mole, hydrogen bonding can be a strong driver of molecular assembly; this is apparent from the dominant role of hydrogen bonding in nucleic-acid base pairing, as well as in the secondary structure of proteins. Carboxylic acid functional groups, which provide two hydrogen bonds, are particularly promising and reliable in creating and maintaining surface order, and self-assembled monolayers of benzoic acids produce structure that depends on the number and relative placement of carboxylic acid groups2,3,4,5,6. Here we use scanning tunnelling microscopy to study self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH), and find that, rather than producing dimeric or linear structures typical of carboxylic acids, FcCOOH forms highly unusual cyclic hydrogen-bonded pentamers, which combine with simultaneously formed FcCOOH dimers to form two-dimensional quasicrystallites that exhibit local five-fold symmetry and maintain translational and rotational order (without periodicity) for distances of more than 400 angstroms.

Neutral CH and cationic CH donor groups as anion receptors.

Abstract: The design and synthesis of anion selective receptors and chemosensors continues to attract considerable interest within the supramolecular community. In recent years, increasing attention has focused on the use of neutral and cationic CH hydrogen bond donors as anion recognition elements. Over the last five years, motifs that support CH⋯X (X = anion) hydrogen bonds have been actively used in various shape persistent macrocycles, foldamers and “molecular machines”. This tutorial review highlights recent developments in host–guest chemistry based on the use of neutral and cationic CH hydrogen bond donors. Also discussed are various structural classifications, including alkyl CH, phenyl CH, triazole-based CH, imidazolium (CH)+ and triazolium (CH)+ hydrogen bond donor systems.

Friedel–Crafts Reaction of Benzyl Fluorides: Selective Activation of C ? F Bonds as Enabled by Hydrogen Bonding

Abstract: A Friedel–Crafts benzylation of arenes with benzyl fluorides has been developed. The reaction produces 1,1-diaryl alkanes in good yield under mild conditions without the need for a transition metal or a strong Lewis acid. A mechanism involving activation of the CF bond through hydrogen bonding is proposed. This mode of activation enables the selective reaction of benzylic CF bonds in the presence of other benzylic leaving groups.

Order–Disorder Transition and Weak Ferromagnetism in the Perovskite Metal Formate Frameworks of [(CH3)2NH2][M(HCOO)3] and [(CH3)2ND2][M(HCOO)3] (M = Ni, Mn)

Abstract: We report the synthesis, crystal structure, thermal, dielectric, Raman, infrared, and magnetic properties of hydrogen and deuterated divalent metal formates, [(CH3)2NH2][M(HCOO)3] and [(CH3)2ND2][M(HCOO)3], where M = Ni, Mn. On the basis of Raman and IR data, assignment of the observed modes to respective vibrations of atoms is proposed. The thermal studies show that for the Ni compounds deuteration leads to a decrease of the phase transition temperature Tc by 5.6 K, whereas it has a negligible effect on Tc in the Mn analogues. This behavior excludes the possibility of proton (deuteron) movement along the N–H···O (N–D···O) bonds as the microscopic origin of the first-order phase transition observed in these crystals below 190 K. According to single-crystal X-ray diffraction, the dimethylammonium (DMA) cations are dynamically disordered at room temperature, because the hydrogen bonds between the NH2 (ND2) groups and the metal-formate framework are disordered. The highly dynamic nature of hydrogen bonds in ...

Iridium-Catalyzed C–H Amination with Anilines at Room Temperature: Compatibility of Iridacycles with External Oxidants

Abstract: Described herein is the development of an iridium-catalyzed direct C–H amination of benzamides with anilines at room temperature, representing a unique example of an Ir catalyst system that is compatible with external oxidants. Mechanistic details, such as the isolation and characterization of key iridacycle intermediates, are also discussed.

The gold–hydrogen bond, Au–H, and the hydrogen bond to gold, Au⋯H–X

Abstract: In the first part of this review, the characteristics of Au–H bonds in gold hydrides are reviewed including the data of recently prepared stable organometallic complexes with gold(I) and gold(III) centers. In the second part, the reports are summarized where authors have tried to provide evidence for hydrogen bonds to gold of the type Au⋯H–X. Such interactions have been proposed for gold atoms in the Au(−I), Au(0), Au(I), and Au(III) oxidation states as hydrogen bonding acceptors and H–X units with X = O, N, C as donors, based on both experimental and quantum chemistry studies. To complement these findings, the literature was screened for examples with similar molecular geometries, for which such bonding has not yet been considered. In the discussion of the results, the recently issued IUPAC definitions of hydrogen bonding and the currently accepted description of agostic interactions have been used as guidelines to rank the Au⋯H–X interactions in this broad range of weak chemical bonding. From the available data it appears that all the intra- and intermolecular Au⋯H–X contacts are associated with very low binding energies and non-specific directionality. To date, the energetics have not been estimated, because there are no thermochemical and very limited IR/Raman and temperature-dependent NMR data that can be used as reliable references. Where conspicuous structural or spectroscopic effects have been observed, explanations other than hydrogen bonding Au⋯H–X can also be advanced in most cases. Although numerous examples of short Au⋯H–X contacts exist in the literature, it seems, at this stage, that these probably make only very minor contributions to the energy of a given system and have only a marginal influence on molecular conformations which so far have most often attracted researchers to this topic. Further, more dedicated investigations will be necessary before well founded conclusions can be drawn.

Anti-electrostatic hydrogen bonds.

Abstract: Ab initio and hybrid density functional techniques were employed to characterize a surprising new class of H-bonded complexes between ions of like charge. Representative H-bonded complexes of both anion-anion and cation-cation type exhibit appreciable kinetic stability and the characteristic theoretical, structural, and spectroscopic signatures of hydrogen bonding, despite the powerful opposition of Coulomb electrostatic forces. All such "anti-electrostatic" H-bond (AEHB) species confirm the dominance of resonance-type covalency ("charge transfer") interactions over the inessential (secondary or opposing) "ionic" or "dipole-dipole" forces that are often presumed to be essential for numerical modeling or conceptual explanation of the H-bonding phenomenon.

The contribution of pseudouridine to stabilities and structure of RNAs

Abstract: Thermodynamic data are reported revealing that pseudouridine ()) can stabilize RNA duplexes when replacing U and forming )-A, )-G, )-U and )-C pairs. Stabilization is dependent on type of base pair, position of ) within the RNA duplex, and type and orientation of adjacent Watson–Crick pairs. NMR spectra demonstrate that for internal )-A, )-G and )-U pairs, the N3 imino proton is hydrogen bonded to the opposite strand nucleotide and the N1 imino proton may also be hydrogen bonded. CD spectra show that general A-helix structure is preserved, but there is some shifting of peaks and changing of intensities. ) has two hydrogen donors (N1 and N3 imino protons) and two hydrogen bond acceptors because the glycosidic bond is C-C rather than C-N as in uridine. This greater structural potential may allow ) to behave as a kind of structurally driven universal base because it can enhance stability relative to U when paired with A, G, U or C inside a double helix. These structural and thermodynamic properties may contribute to the biological functions of ).